I have been to all but three of the bodies of water on this map and found rock pile sites as circled. A pattern is starting to emerge of sites on the eastern sides of ponds.
These ponds are man-made but the topography is natural and the piles could have been built before or after the damming of the waterways. The suggestion seems to be clear: I should go visit the remaining thee ponds.
Correction: I have been to that body of water to the upper right, Hayes Reservoir, and have not found piles on its easter side. More exploration around those ponds is called for.